Documentation

Sequence format

The allowed sequence formats are FASTA and PIR

Example of fasta format:

>HAHU Hemoglobin alpha chain - Human and chimpanzees
VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADAL
TNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASV
STVLTSKYR

Example of pir format:

>P1;HAHU
Hemoglobin alpha chain - Human and chimpanzees
VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADAL
TNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASV
STVLTSKYR*

Databases

Select a database of protein sequences from the list.

Alignment Matrix

The alignment scoring matrix used by Scanps.

Multiple Hits

Scanps can output more than one alternative alignment for each sequence in the score list. Tick this option turn it on.

USA

Select a sequence from a database using the sequence's Uniform Sequence Address (USA). See the EMBOSS documentation on USAs.

Alignment method

standard: Uses simple length-dependent gap penalty affine: Uses an affine gap penalty

Gap opening penalty

For affine gap penalties, this is the penalty for opening a gap in an alignment.

Gap extension (length-dependent) penalty

The penalty for extending gaps in the alignment.

E-value cutoff

Only hits with an Expectation value less than this cutoff are output.

Maximum number of hits to output

The maximum number of hits that is output

E-value cutoff for pairwise alignment output

If this option is ticked, pairwise alignments are output only for hits with E-values above the cutoff.

Maximum number of output pairwise alignments

Set the maximum number of pairwise alignments output.

Pairwise alignment width

Define the width of the pairwise alignments in the output.

E-value for profile inclusion

This sets the E-value cutoff for including sequences in the multiple alignment profile that is built from the first and subsequent iterations of a scan. This is usually set to be much smaller than the E-value cutoff for the output list.

Number of iterations

Number of search iterations. If this is greater than 1, scanps will build a search profile from the results of the initial scan and scan the database with this profile. This process is repeated N times where N is the number of iterations. The search may also stop if two successive iterations return the same set of sequences.

Print frequency table

Output the frequency table calculated from the multiple alignment in each iteration.

Print-profile

Tick this option to include the profile tables in the output. These profile table are calculated from the multiple alignments in each iteration and used to search in the next iteration.

Raw output

Tick this option to get the raw Scanps output without any HTML formatting.